NHacker Next
  • new
  • past
  • show
  • ask
  • show
  • jobs
  • submit
Show HN: Modeling the human body in Rust so I can cmd+click through it (github.com)
dleeftink 120 days ago [-]
If you're looking for a 'click-through' experience, the JKU vis lab has long provided some awesome tools and visuals (ca. 2009) for interacting with the human genome[0][1].

[0]: https://jku-vds-lab.at/tools/

[1]: https://jku-vds-lab.at/publications/2009_bioinformatics_cale...

lleong1618 120 days ago [-]
amazing and its open source thanks fro bring this up.
dleeftink 120 days ago [-]
Some sophisticated tools coming out of that lab, I wish we could we could put more effort towards developing tools similar to their embedding explorer[0].

[0]: https://youtu.be/yBCe8SqGwK8

pacoWebConsult 120 days ago [-]
Any grounding in medical truth/ is anything sourced to legitimate references or is this entirely pulled from the model's general training of human anatomy?
lovecg 120 days ago [-]
100k lines in one day of “coding”? I think you already know the answer.
lleong1618 120 days ago [-]
exactly, i mean can attach a research agent to each file or commit to validate and confirm the values, which would just give validity to internet information I guess.
lleong1618 120 days ago [-]
I am pulling from the model and was thinking of attaching a research agent on per file to validate each file and adding sourced validated information.

it seems sound to get structure but on real values and source grounding is needed to be validated.

just a poc

jll29 120 days ago [-]
I wasn't sure what to expect, so I opened a random bit of the code.

                Some(Ancestry::Ashkenazi) => Self {
                    ancestry,
                    lactose_restricted: false,
                    alcohol_restriction_level: AlcoholRestrictionLevel::Moderate,
                    vitamin_d_supplementation_iu: 800.0,
                    recommended_foods: vec![
                        "Fish".to_string(),
                        "Whole grains".to_string(),
                        "Vegetables".to_string(),
                        "Olive oil".to_string(),
                        "Nuts".to_string(),
                    ],
                    foods_to_limit: vec![
                        "High-fat dairy".to_string(),
                        "Processed meats".to_string(),
                    ],
Now this seems to mix a couple of things in the same module: I would suggest to separate out dietary views from a model of the human body and its genetic heritage.

Scientific views may change over time based on new results, and even body properties like blood pressure or BMI are not constant per person but bound to vary; so perhaps a Body should be modeled as a view or snapshot of a set of time series?

I would like to encourage you to take a scientist's view: if you had not just one (your own) but two models, how would you evaluate which is "better" - in other words the evaluation question. You could set a particular task and perhaps finding out something works better with your model than with a full-text index of the textbook you used and a simple Lucene search interface?

Are you planning to connect your model to any kind of visualization? Should be useful.

rafram 120 days ago [-]
Hah. Ashkenazis marked as not being lactose-intolerant? Interesting stuff.
ShrimpHawk 120 days ago [-]
The entire project is AI coded. Thought of this level was not put into developing it.
120 days ago [-]
jstrieb 120 days ago [-]
This project reminds me of Matt Might's work (predating LLMs) on using techniques from Precision Medicine to help his son, who had a rare disease.

https://www.youtube.com/watch?v=Rt3XyeFHvt4 (poorly transcribed here: https://www.janestreet.com/tech-talks/algorithm-for-precisio...)

If I recall correctly, he used miniKanren along with formalized, structured data extracted from medical research. Unfortunately, his son has since passed away.

lleong1618 120 days ago [-]
This is an incredible story, heart goes out to him. He has done some amazing work from this information.

There's nothing that is not actionable, you can always do science.

rfl890 120 days ago [-]
How do we know this is accurate and not some big hallucination? Is the data sourced anywhere? Has anyone with a relevant background even skimmed through the code? It seems like a great idea in theory, but this execution is worrying.
lleong1618 120 days ago [-]
Yes, It's very much a "I wonder if this would work" and kinda did. to be taken in some what of a regard would be attaching a research agent on each commit.

I did spot checks on random files with research agents and it seems to be ok for a claude code loop.

I'm not a Dr'

Please! is anyone a DR

rfl890 120 days ago [-]
I mean, it is a pretty cool idea, but trusting an LLM to correctly implement an entire human body in software is a recipe for disaster. There's bound to be tons of hallucinations and errors.
lleong1618 120 days ago [-]
absolutely agree but for the purposes of working out what ALDH2 deficiency is and clicking through it was successful

should absolutely have a research agent or eyes on for hallucinations and errors

JumpCrisscross 120 days ago [-]
> for the purposes of working out what ALDH2 deficiency is and clicking through it was successful

Does your code model acetaldehyde metabolism?

The exercise is an interesting proof of concept for a click-through model of a biological system. But it's also a warning for trusting LLMs for understanding.

lleong1618 120 days ago [-]
no it didn't do click through for this metabolism at first but it read your comment and then added it I guess. "examples/acetaldehyde_metabolism.rs" its about to push this in a moment
JumpCrisscross 120 days ago [-]
> its about to push this in a moment

The point is acetaldehyde metabolism is at the heart of your question: Why do some people flush red with alcohol.

Reading the first reference on Wikipedia's article about alcohol flushing [1][2] would have generated, I believe, more understanding about the biochemistry involved. (And the fact that ALDH2 deficiency simply exacerbates something we all do--acetaldehyde is a big part of what causes hangovers.)

What that would not have done is demonstrate (a) a genuinely interesting way to "step through" a physical system and (b) the ease with which a biochemist might be able to do so. As a hack and a project and a mode of communicating a model, I love this. Where I'm objecting is in pitching it per se as a mode for understanding a phenomenon, in this case, "what ALDH2 deficiency is."

[1] https://en.wikipedia.org/wiki/Alcohol_flush_reaction#cite_no...

[2] https://pmc.ncbi.nlm.nih.gov/articles/PMC2659709/

koakuma-chan 120 days ago [-]
I think it's time to learn to stop publishing clearly fully AI generated "projects." Anyone can pull up CC and type "model the human body in Rust," or whatever.
jvanderbot 120 days ago [-]
The old "Look what I built" thread has really bifurcated into "here's what I painstakingly crafted and maybe some lessons learned" and "look what I asked AI to make and it worked".

The latter feels a bit less hacker. Akin to saying "I got someone on fiver to mod this game look how cool it is". Sure, ideas are something, but as AI gets better this is less hacker and more just "Tool worked".

lleong1618 120 days ago [-]
Ai will replace more of what we are doing, but I had fun with this so I thought I would share
jvanderbot 120 days ago [-]
More about the framing - if you posted ai imagery in a "cool imagery" sub, you'd probably be fine. If you posted it in a painting sub, that's probably no bueno.

I came to HN for "cool software" and "software as a craft/art", but they are being muddled here with a blanket ShowHN type demo.

moron4hire 120 days ago [-]
The AI bubble will pop, nobody will be able to afford AI code completion without VC money subsidizing companies like Anthropic, and it will all go the way of UML tools: A thing one old guy the company in short sleeved, plaid shirts, cargo khakis, and a George Lucas haircut keeps insisting is the future 20 years later.
koakuma-chan 120 days ago [-]
I think this is an outdated view. People are already running local models for code completion, and it will not be much longer until you can run code agents locally as well.
nomilk 120 days ago [-]
That was my first impression too, but not my conclusion. A project of this scale would take years if not for AI assistance, and OP is absolutely not trying to pass this off as a medical tool developed by professionals, but as a fun learning tool and interesting application of type systems and agents to solve a problem.
lleong1618 120 days ago [-]
nomilk gets it.

This is 100% a hack and fun learning tool. It is an experiment to see if modeling biological processes with rust (leveraging specifically its strong type system)

and to see what agents can do. In fact the agent is listening to this thread and taking feed back and changing the repo.

jvanderbot 120 days ago [-]
I appreciate this I really do.

But how will you see if modelling biological processes with rust actually benefits from a strong type system? What have you learned from this? Vs what have you read from the promises of the chatbot?

I don't mean to be dismissive but I think the real goal is "make something cool with an AI agent" and that's fine. But be honest

tehlike 120 days ago [-]
This is hackernews, this is the place for people to hack stuff, and share.
lleong1618 120 days ago [-]
Yes this is 100% a hack.
120 days ago [-]
lleong1618 120 days ago [-]
maybe putting - Ai as a tag might help? but this is 100% a hack and experiment for fun. Test out what agents can do and can we model bio with rust.
overtone1000 120 days ago [-]
I wonder how much it would cost to pay a domain expert to review 95k lines of code. As a domain expert who codes for fun and loves rust, I can only say the answer is, "A lot."
HeavyStorm 120 days ago [-]
Clickable? Like a... Hyperlink?

After the "this meeting could have been an email", we get the "code could have been html"

WillAdams 120 days ago [-]
For a physical spin on this sort of thing in OpenSCAD, see:

https://github.com/davidson16807/relativity.scad/wiki/Human-...

sixo 120 days ago [-]
the absurd things people come up with to meet their own needs are usually good indicators of products and services which want to exist
dietr1ch 120 days ago [-]
True, but to me it seems the product is halfway there with org-roam/logseq/obsidian and that Rust code is the wrong way to start building it.

I'd try generating markdown to be rendered in logseq by teaching the AI how to link and whatnot in my AGENT.md (or whatever people call their project-local instruction/context file).

From outside, I'd not trust hallucinated stuff, but it'd be neat to start a project where knowledgeable humans did oversee all the proposed changes.

sixo 120 days ago [-]
well yeah this is not itself the product, this is a demonstration of the need

Obsidian/etc really isn't it either, though; clearly OP wants to be able to do calculations with this stuff. They want both the knowledge graph AND an executable code environment. (I imagine Emacs can do both.)

But think more broadly. Imagine just

```

import <established knowledge>.anatomy

import <established knowledge>.high_energy_physics

import <established knowledge>.microeconomics

...

```

into a notebook-like environment, with good intellisense and completions. But not quite as a programming language—somewhere between that and a wiki.

sixo 120 days ago [-]
Similar: for years I've been lugging around the idea of making a game like Civilization but where all of the different theories of history can be turned on/off as modules. Maybe going back to prehistory:

- did fire lead to cooking lead to big brains lead to tools lead to agriculture?

- or was it ice ages ending that lead to agriculture?

- or did oxygen levels change leading to more efficient brains?

- or were we Born to Run?

- or did women's hips change shapes to allow bigger brains?

- or perhaps 2001: A Space Odyssey occurred as written

- or Ancient Aliens...

Repeat for every other highly-debated period of history.

Somehow having all of these in the same modular system feels like it would metabolize them in a way that reading a bunch of separate theories can't really do. Same for OP's anatomy.

pagekicker 120 days ago [-]
like this idea. Add "tech trees": path dependence can be arbitrary. What if we kept going with vacuum tubes/no transistors?
lleong1618 120 days ago [-]
Yeah ahaha, I mean I just needed 2 pieces of information and got carried away. But would be awesome to have a runnable human emulation.
csunoser 120 days ago [-]
Maybe this is the future. But I dread looking at perfectly formatted yet sterile readme with too many emojis for comfort.
moron4hire 120 days ago [-]
It's one emoji
csunoser 120 days ago [-]
I mean, literally not true. There are 7. The problem is that most of the emojis there don't do anything for the content.

Emojis are not the core problem. Mindlessly letting claude do the work and then farm karma on HN is.

moron4hire 120 days ago [-]
Your reply mentioned "perfectly formatted yet sterile", which could just be someone paying more than 10 minutes of attention to the damn thing, and the emoji. The way you made it sound, it was full of smileys and trees and rocket ships. It's one check mark emoji used in a list of 5 items and at the end of 2 headers. You didn't say anything about Claude.
csunoser 120 days ago [-]
It seems like you think the author wrote this by hand and paid a great deal attention.

What do you think is the chance that claude code wrote the readme?

stronglikedan 120 days ago [-]
I have an Asian friend that gets flushed when drinking, but I didn't know it was an Asian thing. TIL
120 days ago [-]
lleong1618 117 days ago [-]
updates on learnings - the feed back from hn about ground truths was helpful passed this thread into the ai and it started to base truth on exa search. - it produced alot of slop so it added a review cycle to remove alot of the slop. - it worked out it was doing performative work then removed the data as code and moved this to toml. it then started to focus heavy on processes and doing things like the ALDH2 metabolic process.

honest take - decent at getting a quick understanding of what the ALDH2 process is like but struggles with harder modelling, the experiment gave better insights into ai then medical. (slop is countable with exa mcp (ground truthing, research, anti hallucinations).

Guidelines | FAQ | Lists | API | Security | Legal | Apply to YC | Contact
Rendered at 14:56:55 GMT+0000 (Coordinated Universal Time) with Vercel.